Locus 4234

Sequence ID	3L_DroMel_CAF1
Location	12,388,649 – 12,388,763
Length	114
Max. P	0.999604

overview

Window 3

Location	12,388,649 – 12,388,763
Length	114
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	93.88
Mean single sequence MFE	-31.69
Consensus MFE	-29.53
Energy contribution	-28.49
Covariance contribution	-1.04
Combinations/Pair	1.17
Mean z-score	-2.23
Structure conservation index	0.93
SVM decision value	3.77
SVM RNA-class probability	0.999604
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12388649 114 + 23771897
UACUGGUCGAGCUAUUUAAGAGUUCGUCUGCUUUUACGCUAUUUCGGCGACUUUGUGGCUUAAAGCGAUUCACGCAGAACUCUUCAAUUUUAAUUU-UUUGGGUUUGCCAGUGUG
((((((.((((((....((((((((.......((((.(((((...(....)...))))).))))(((.....))).))))))))(((.........-.))))))))))))))).. ( -33.30)
>DroSec_CAF1 15102 114 + 1
UACUGGUCAAACUAUUUAAGAGUUCGUCUGCUUUUACGCUAAUUCGGCGACUUUAUGGCUUAAAGCGAUUUACGCAGAACUCUUUAAUUUUAAUUU-UUUGGGUUUGCCAGUGUG
((((((.((((((....(((((((((((........((((.....)))).......))).....(((.....))).))))))))............-....)))))))))))).. ( -31.61)
>DroSim_CAF1 15228 114 + 1
UACUGGUCGAGCUAUUUAAGAGUUCGUCUGCUUUUACGCUAUUUCGGCGACUUUAUGGCUUAAAGCGAUUCACGCAGAACUCUUUAAUUUUAAUUU-UUUGGGUUUGCCAGUGUG
((((((.((((((....((((((((.......((((.(((((...(....)...))))).))))(((.....))).))))))))............-....)))))))))))).. ( -32.35)
>DroEre_CAF1 15055 115 + 1
UACUGGUCGAGCUAUUCAAGAGUUCGUCUGGUUUUACGCUAUUGCGGCGACUUUAUGGCUUAACGCGAUUCACACAGAACUCUUAAAUUUUAAUUUUUUUGGGUUUGCCAGUGUG
((((((.((((((....((((((((((..((((...(((....)))..))))..)).((.....))..........))))))))......(((.....))))))))))))))).. ( -30.10)
>DroYak_CAF1 15306 114 + 1
UACUGGUCGAGCUGUUCAAGAGUUCGUCUGGUUUUACGCUAUUUCGGCGGCUUUAUGGCUUUAAGCGAUUCACACAGAACUCUUAAAUUUUAAUUU-UUUGGGUUUGCCAGUGUG
((((((.(((((((((.((((((((((.(((.....((((.....))))((((.........))))...))).)).)))))))).)))........-....)))))))))))).. ( -31.10)
>consensus
UACUGGUCGAGCUAUUUAAGAGUUCGUCUGCUUUUACGCUAUUUCGGCGACUUUAUGGCUUAAAGCGAUUCACGCAGAACUCUUAAAUUUUAAUUU_UUUGGGUUUGCCAGUGUG
((((((.(((((((((.((((((((((.((......((((.....)))).....((.((.....)).)).)).)).)))))))).))).............)))))))))))).. (-29.53 = -28.49 +  -1.04)

alignment

secondary structure

dotplot

Window 4

Location	12,388,649 – 12,388,763
Length	114
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	93.88
Mean single sequence MFE	-24.21
Consensus MFE	-18.60
Energy contribution	-18.36
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-2.03
Structure conservation index	0.77
SVM decision value	0.58
SVM RNA-class probability	0.788675
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12388649 114 - 23771897
CACACUGGCAAACCCAAA-AAAUUAAAAUUGAAGAGUUCUGCGUGAAUCGCUUUAAGCCACAAAGUCGCCGAAAUAGCGUAAAAGCAGACGAACUCUUAAAUAGCUCGACCAGUA
...((((((.....(((.-.........)))(((((((((((......((((....((.((...)).))......)))).....)))))...)))))).........).))))). ( -23.40)
>DroSec_CAF1 15102 114 - 1
CACACUGGCAAACCCAAA-AAAUUAAAAUUAAAGAGUUCUGCGUAAAUCGCUUUAAGCCAUAAAGUCGCCGAAUUAGCGUAAAAGCAGACGAACUCUUAAAUAGUUUGACCAGUA
...((((((((((.....-.(((....))).(((((((((((.......((((((.....))))))(((.......))).....)))))...)))))).....))))).))))). ( -26.70)
>DroSim_CAF1 15228 114 - 1
CACACUGGCAAACCCAAA-AAAUUAAAAUUAAAGAGUUCUGCGUGAAUCGCUUUAAGCCAUAAAGUCGCCGAAAUAGCGUAAAAGCAGACGAACUCUUAAAUAGCUCGACCAGUA
...((((((.........-.(((....))).(((((((((((.......((((((.....))))))(((.......))).....)))))...)))))).........).))))). ( -21.60)
>DroEre_CAF1 15055 115 - 1
CACACUGGCAAACCCAAAAAAAUUAAAAUUUAAGAGUUCUGUGUGAAUCGCGUUAAGCCAUAAAGUCGCCGCAAUAGCGUAAAACCAGACGAACUCUUGAAUAGCUCGACCAGUA
...((((((.......((....))...((((((((((((.((.((....(((..............)))(((....)))......)).)))))))))))))).....).))))). ( -25.34)
>DroYak_CAF1 15306 114 - 1
CACACUGGCAAACCCAAA-AAAUUAAAAUUUAAGAGUUCUGUGUGAAUCGCUUAAAGCCAUAAAGCCGCCGAAAUAGCGUAAAACCAGACGAACUCUUGAACAGCUCGACCAGUA
...(((((..........-.........(((((((((((.((.((....((((.........))))(((.......)))......)).)))))))))))))(.....).))))). ( -24.00)
>consensus
CACACUGGCAAACCCAAA_AAAUUAAAAUUAAAGAGUUCUGCGUGAAUCGCUUUAAGCCAUAAAGUCGCCGAAAUAGCGUAAAAGCAGACGAACUCUUAAAUAGCUCGACCAGUA
...((((((...........(((....))).((((((((.(((.....)))...............(((.......)))...........)))))))).........).))))). (-18.60 = -18.36 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:24 2006